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Detection of B.1.351 SARS-CoV-2 Variants strain — Zambia, December 2020
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February 17, 2021
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Description:The first laboratory-confirmed cases of coronaVirus disease 2019 (COVID-19), the illness caused by SARS-CoV-2, in Zambia were detected in March 2020 (1). Beginning in July, the number of confirmed cases began to increase rapidly, first peaking during July–August, and then declining in September and October (Figure). After 3 months of relatively low case counts, COVID-19 cases began rapidly rising throughout the country in mid-December. On December 18, 2020, South Africa published the genome of a SARS-CoV-2 Variants strain with several mutations that affect the spike protein (2). The Variants included a mutation (N501Y) associated with increased transmissibility.†,§ SARS-CoV-2 lineages with this mutation have rapidly expanded geographically.¶,** The Variants strain (PANGO [Phylogenetic Assignment of Named Global Outbreak] lineage B.1.351††) was first detected in the Eastern Cape Province of South Africa from specimens collected in early August, spread within South Africa, and appears to have displaced the majority of other SARS-CoV-2 lineages circulating in that country (2). As of January 10, 2021, eight countries had reported cases with the B.1.351 Variants. In Zambia, the average number of daily confirmed COVID-19 cases increased 16-fold, from 44 cases during December 1–10 to 700 during January 1–10, after detection of the B.1.351 Variants in specimens collected during December 16–23. Zambia is a southern African country that shares substantial commerce and tourism linkages with South Africa, which might have contributed to the Transmission of the B.1.351 Variants between the two countries.
Since September 2020, University of Zambia and PATH (https://www.path.orgexternal icon) have routinely been conducting genetic epidemiologic studies using whole genome sequencing (WGS) on SARS-CoV-2–positive specimens. A subset of specimens collected during March 18–December 23, 2020, were sequenced, from which 268 high-quality genomes were generated. Specimens were selected for WGS based on availability and real-time reverse transcription–polymerase chain reaction (RT-PCR) diagnostic test cycle threshold (Ct) values of <30; lower Ct values are correlated with larger amounts of Virus in the sample. Sequences were linked to case investigation information including patient age, sex, and geographic location from routine public health data maintained by the Zambia National Public Health Institute. For WGS, complementary DNA was prepared using random primers from viral RNA extracted from SARS-CoV-2 real-time RT-PCR–positive specimens. Multiplex PCR was then performed using custom primers (3) to generate overlapping amplicons for nanopore sequencing on a MinION (Oxford Nanopore Technology, United Kingdom).§§ Consensus sequence reads were generated using the standard ARTIC Network bioinformatic pipeline,¶¶ a system for processing samples from viral disease outbreaks to generate real-time, actionable epidemiologic information.
Suggested citation for this article: Mwenda M, Saasa N, Sinyange N, et al. Detection of B.1.351 SARS-CoV-2 Variant Strain — Zambia, December 2020. MMWR Morb Mortal Wkly Rep. ePub: 17 February 2021.
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